Rigid-body random translate/rotate around centroid of downstream side of a jump. More...

#include <RigidBodyMover.hh>

Inheritance diagram for protocols::rigid::RigidBodyMover:

Collaboration diagram for protocols::rigid::RigidBodyMover:

Public Types
typedef ThermodynamicMover	parent

Public Member Functions
	RigidBodyMover ()

	RigidBodyMover (int const rb_jump_in, Direction dir_in=n2c)

	RigidBodyMover (RigidBodyMover const &src)

virtual	~RigidBodyMover ()

void	rot_center (core::Vector const rot_center_in)
	Manual override of rotation center. More...

virtual void	apply (core::pose::Pose &pose)=0

virtual std::string	get_name () const
	Each derived class must specify its name. The class name. More...

virtual bool	preserve_detailed_balance () const
	get whether detailed balance is preserved (i.e. no branch angle optimization during moves) More...

virtual void	set_preserve_detailed_balance (bool)
	set whether detailed balance is preserved (i.e. no branch angle optimization during moves) More...

virtual utility::vector1 < core::id::TorsionID_Range >	torsion_id_ranges (core::pose::Pose &pose)
	get the TorsionIDs perturbed by the mover during moves, along with their ranges More...

int	rb_jump () const

void	rb_jump (int jump_id)

void	unfreeze ()

void	freeze ()

Public Member Functions inherited from protocols::canonical_sampling::ThermodynamicMover
	ThermodynamicMover ()

virtual	~ThermodynamicMover ()

virtual void	initialize_simulation (core::pose::Pose &pose, protocols::canonical_sampling::MetropolisHastingsMover const &metropolis_hastings_mover, core::Size cycle)
	callback executed before any Monte Carlo trials More...

virtual void	observe_after_metropolis (protocols::canonical_sampling::MetropolisHastingsMover const &metropolis_hastings_mover)
	callback executed after the Metropolis criterion is evaluated More...

virtual core::Real	last_proposal_density_ratio ()
	callback for proposal density ratio of last apply method More...

virtual void	finalize_simulation (core::pose::Pose &pose, protocols::canonical_sampling::MetropolisHastingsMover const &metropolis_hastings_mover)
	callback executed after all Monte Carlo trials More...

virtual bool	is_multi_trial ()
	determine whether the move performs multiple trials on a single apply More...

virtual core::Real	last_inner_score_temperature_delta ()
	get change in internal score/temperature for last apply method of multiple trial movers More...

virtual protocols::canonical_sampling::MetropolisHastingsMoverAP	metropolis_hastings_mover ()
	get the MetropolisHastingsMover for multiple trial movers More...

virtual void	set_metropolis_hastings_mover (protocols::canonical_sampling::MetropolisHastingsMoverAP metropolis_hastings_mover)
	set the MetropolisHastingsMover for multiple trial movers More...

virtual utility::vector1 < core::id::DOF_ID_Range >	dof_id_ranges (core::pose::Pose &pose)
	get the DOF_IDs perturbed by the mover during moves (not including those returned by torsion_id_ranges(), along with their ranges More...

Public Member Functions inherited from protocols::moves::Mover
	Mover ()

virtual	~Mover ()

virtual MoverSP	create ()

virtual void	apply (core::io::serialization::PipeMap &pmap)

virtual void	parse_state (SerializableState const &state)

virtual void	parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)

virtual void	save_state (SerializableState &state)

	Mover (std::string const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...

	Mover (Mover const &other)

Mover &	operator= (Mover const &other)
	assignment operator More...

std::string const &	type () const

std::string	get_current_tag () const
	A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More...

void	set_current_tag (std::string const &new_tag)

virtual void	set_input_pose (PoseCOP pose)
	setter for poses contained for rms More...

virtual void	set_native_pose (PoseCOP pose)
	setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...

PoseCOP	get_input_pose () const

PoseCOP	get_native_pose () const

virtual void	test_move (Pose &pose)
	: Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...

void	type (const std::string &type_in)

virtual MoverOP	clone () const
	clone has to be overridden only if clone invocation is expected. More...

virtual void	parse_my_tag (TagPtr const tag, DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

std::string	get_type () const

MoverStatus	get_last_move_status () const
	end parser interface, start Job Distributor interface///////////// More...

void	reset_status ()
	resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More...

virtual core::pose::PoseOP	get_additional_output ()
	Mechanism by which a mover may return multiple output poses from a single input pose. More...

virtual void	clear_info ()
	Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More...

virtual Strings &	info ()
	non-const accessor More...

virtual Strings const &	info () const
	const accessor More...

virtual bool	reinitialize_for_each_job () const
	this function informs the job distributor (august 08 vintage) whether this object needs to be freshly regenerated on each use. More...

virtual bool	reinitialize_for_new_input () const
	this function informs the job distributor (august 08 vintage) whether this object needs to be regenerated when the input pose is about to change (for example, if the mover has special code on the first apply() that is only valid for that one input pose). More...

virtual MoverOP	fresh_instance () const
	this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More...

void	set_current_job (protocols::jobdist::BasicJobCOP job)

jobdist::BasicJobCOP	get_current_job () const

Protected Attributes
int	rb_jump_

Direction	dir_
	direction of folding (n-term to c-term) More...

core::Vector	rot_center_
	center of rotation More...

bool	freeze_

Additional Inherited Members
Static Public Member Functions inherited from protocols::moves::Mover
static std::string	name ()

static void	register_options ()
	overload this static method if you access options within the mover. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. More...

Protected Member Functions inherited from protocols::moves::Mover
void	set_last_move_status (MoverStatus status)
	nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More...

Detailed Description

Rigid-body random translate/rotate around centroid of downstream side of a jump.

We operate on a single jump rather than e.g. a randomly selected jump from the mobile jumps in a MoveMap. If you want a random choice among jumps, put multiple RigidBodyMovers into a RandomMover (which will give you more control, anyway).

Definition at line 75 of file RigidBodyMover.hh.

Member Typedef Documentation

typedef ThermodynamicMover protocols::rigid::RigidBodyMover::parent

Definition at line 77 of file RigidBodyMover.hh.

Constructor & Destructor Documentation

protocols::rigid::RigidBodyMover::RigidBodyMover ( )

Definition at line 68 of file RigidBodyMover.cc.

protocols::rigid::RigidBodyMover::RigidBodyMover	(	int const	rb_jump_in,
		Direction	dir_in = `n2c`
	)

Definition at line 76 of file RigidBodyMover.cc.

References protocols::rigid::c2n, dir_, protocols::rigid::n2c, and protocols::rigid::random.

protocols::rigid::RigidBodyMover::RigidBodyMover ( RigidBodyMover const & src)

Definition at line 91 of file RigidBodyMover.cc.

protocols::rigid::RigidBodyMover::~RigidBodyMover ( )

virtual

Definition at line 100 of file RigidBodyMover.cc.

Member Function Documentation

virtual void protocols::rigid::RigidBodyMover::apply ( core::pose::Pose & pose)

pure virtual

Implements protocols::moves::Mover.

void protocols::rigid::RigidBodyMover::freeze ( )

inline

Definition at line 133 of file RigidBodyMover.hh.

References freeze_.

Referenced by protocols::ligand_docking::Translate::uniform_translate_ligand().

std::string protocols::rigid::RigidBodyMover::get_name ( ) const

virtual

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

Definition at line 103 of file RigidBodyMover.cc.

virtual bool protocols::rigid::RigidBodyMover::preserve_detailed_balance ( ) const

inlinevirtual

get whether detailed balance is preserved (i.e. no branch angle optimization during moves)

Implements protocols::canonical_sampling::ThermodynamicMover.

Definition at line 102 of file RigidBodyMover.hh.

int protocols::rigid::RigidBodyMover::rb_jump ( ) const

inline

Definition at line 129 of file RigidBodyMover.hh.

References rb_jump_.

Referenced by protocols::rigid::operator<<(), and protocols::ligand_docking::Translate::uniform_translate_ligand().

void protocols::rigid::RigidBodyMover::rb_jump ( int jump_id)

inline

Definition at line 130 of file RigidBodyMover.hh.

References rb_jump_.

void protocols::rigid::RigidBodyMover::rot_center ( core::Vector const rot_center_in)

inline

Manual override of rotation center.

Definition at line 95 of file RigidBodyMover.hh.

References rot_center_.

virtual void protocols::rigid::RigidBodyMover::set_preserve_detailed_balance ( bool )

inlinevirtual

set whether detailed balance is preserved (i.e. no branch angle optimization during moves)

Implements protocols::canonical_sampling::ThermodynamicMover.

Definition at line 107 of file RigidBodyMover.hh.

utility::vector1< core::id::TorsionID_Range > protocols::rigid::RigidBodyMover::torsion_id_ranges ( core::pose::Pose & pose)

virtual

get the TorsionIDs perturbed by the mover during moves, along with their ranges

Implements protocols::canonical_sampling::ThermodynamicMover.

Definition at line 108 of file RigidBodyMover.cc.

void protocols::rigid::RigidBodyMover::unfreeze ( )

inline

Definition at line 132 of file RigidBodyMover.hh.

References freeze_.

Member Data Documentation

Direction protocols::rigid::RigidBodyMover::dir_

protected

direction of folding (n-term to c-term)

Definition at line 120 of file RigidBodyMover.hh.

Referenced by protocols::enzdes::PredesignPerturbMover::apply(), protocols::rigid::RigidBodyPerturbMover::apply(), protocols::rigid::RigidBodyPerturbNoCenterMover::apply(), protocols::rigid::RigidBodyRandomizeMover::apply(), protocols::rigid::RigidBodySpinMover::apply(), protocols::rigid::RigidBodyDeterministicSpinMover::apply(), protocols::rigid::RigidBodyDofPerturbMover::apply(), RigidBodyMover(), and protocols::rigid::RigidBodyPerturbNoCenterMover::RigidBodyPerturbNoCenterMover().

bool protocols::rigid::RigidBodyMover::freeze_

protected

Definition at line 124 of file RigidBodyMover.hh.

Referenced by protocols::rigid::RigidBodyPerturbMover::apply(), protocols::rigid::RigidBodyRandomizeMover::apply(), protocols::rigid::UniformSphereTransMover::apply(), freeze(), and unfreeze().

int protocols::rigid::RigidBodyMover::rb_jump_

protected

Definition at line 118 of file RigidBodyMover.hh.

core::Vector protocols::rigid::RigidBodyMover::rot_center_

protected

center of rotation

Definition at line 123 of file RigidBodyMover.hh.

Referenced by protocols::enzdes::PredesignPerturbMover::apply(), protocols::rigid::RigidBodyPerturbMover::apply(), protocols::rigid::RigidBodyRandomizeMover::apply(), protocols::rigid::RigidBodySpinMover::apply(), protocols::rigid::RigidBodyDeterministicSpinMover::apply(), protocols::rigid::RigidBodyDeterministicSpinMover::RigidBodyDeterministicSpinMover(), protocols::rigid::RigidBodyRandomizeMover::RigidBodyRandomizeMover(), rot_center(), and protocols::rigid::RigidBodySpinMover::rot_center().

The documentation for this class was generated from the following files:

src/protocols/rigid/RigidBodyMover.hh
src/protocols/rigid/RigidBodyMover.cc

Public Types

Public Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation